Pandit: a database of protein and associated nucleotide domains with inferred trees. Export

@article{citeulike:2814222, abstract = {MOTIVATION: A large, high-quality database of homologous sequence alignments with good estimates of their corresponding phylogenetic trees will be a valuable resource to those studying phylogenetics. It will allow researchers to compare current and new models of sequence evolution across a large variety of sequences. The large quantity of data may provide inspiration for new models and methodology to study sequence evolution and may allow general statements about the relative effect of different molecular processes on evolution. RESULTS: The Pandit 7.6 database contains 4341 families of sequences derived from the seed alignments of the Pfam database of amino acid alignments of families of homologous protein domains (Bateman et al., 2002). Each family in Pandit includes an alignment of amino acid sequences that matches the corresponding Pfam family seed alignment, an alignment of DNA sequences that contain the coding sequence of the Pfam alignment when they can be recovered (overall, 82.9\% of sequences taken from Pfam) and the alignment of amino acid sequences restricted to only those sequences for which a DNA sequence could be recovered. Each of the alignments has an estimate of the phylogenetic tree associated with it. The tree topologies were obtained using the neighbor joining method based on maximum likelihood estimates of the evolutionary distances, with branch lengths then calculated using a standard maximum likelihood approach.}, address = {Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. simon@ebi.ac.uk}, author = {Whelan, S. and de Bakker, P. I. and Goldman, N.}, citeulike-article-id = {2814222}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btg188}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/12/1556}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12912837}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12912837}, day = {12}, doi = {10.1093/bioinformatics/btg188}, issn = {1367-4803}, journal = {Bioinformatics (Oxford, England)}, keywords = {alignment, amino-acid, databases, dna, evolution, homology, likelihood, methods, models, phylogenomics, phylogeny, phyloinformatics, protein, proteins, sequence}, month = {August}, number = {12}, pages = {1556--1563}, posted-at = {2008-12-18 02:07:34}, priority = {2}, title = {Pandit: a database of protein and associated nucleotide domains with inferred trees.}, url = {http://dx.doi.org/10.1093/bioinformatics/btg188}, volume = {19}, year = {2003} }

TY - JOUR ID - citeulike:2814222 L3 - citeulike-article-id:2814222 N2 - MOTIVATION: A large, high-quality database of homologous sequence alignments with good estimates of their corresponding phylogenetic trees will be a valuable resource to those studying phylogenetics. It will allow researchers to compare current and new models of sequence evolution across a large variety of sequences. The large quantity of data may provide inspiration for new models and methodology to study sequence evolution and may allow general statements about the relative effect of different molecular processes on evolution. RESULTS: The Pandit 7.6 database contains 4341 families of sequences derived from the seed alignments of the Pfam database of amino acid alignments of families of homologous protein domains (Bateman et al., 2002). Each family in Pandit includes an alignment of amino acid sequences that matches the corresponding Pfam family seed alignment, an alignment of DNA sequences that contain the coding sequence of the Pfam alignment when they can be recovered (overall, 82.9% of sequences taken from Pfam) and the alignment of amino acid sequences restricted to only those sequences for which a DNA sequence could be recovered. Each of the alignments has an estimate of the phylogenetic tree associated with it. The tree topologies were obtained using the neighbor joining method based on maximum likelihood estimates of the evolutionary distances, with branch lengths then calculated using a standard maximum likelihood approach. IS - 12 JF - Bioinformatics (Oxford, England) SN - 1367-4803 AD - Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. simon@ebi.ac.uk EP - 1563 TI - Pandit: a database of protein and associated nucleotide domains with inferred trees. VL - 19 SP - 1556 KW - alignment KW - amino-acid KW - databases KW - dna KW - evolution KW - homology KW - likelihood KW - methods KW - models KW - phylogenomics KW - phylogeny KW - phyloinformatics KW - protein KW - proteins KW - sequence AU - Whelan, S AU - de Bakker, PI AU - Goldman, N PY - 2003/08/12/ UR - http://dx.doi.org/10.1093/bioinformatics/btg188 ER -